Popular multiple alignment software
MUSCLE is one of the most widely-used methods in biology. On average, MUSCLE is cited by seven new papers every day.

Fast, accurate and easy to use
MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks.
 
Papers
There are two papers. The first (NAR) introduced the algorithm, and is the primary citation if you use the program. The second (BMC Bioinformatics) gives more technical details, including descriptions of non-default options.

Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput
  Nucleic Acids Res. 32(5):1792-1797 [Link to PubMed].

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity
  BMC Bioinformatics, (5) 113 [Link to PubMed].